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- PDB-1jlj: 1.6 Angstrom crystal structure of the human neuroreceptor anchori... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jlj | ||||||
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Title | 1.6 Angstrom crystal structure of the human neuroreceptor anchoring and molybdenum cofactor biosynthesis protein gephyrin | ||||||
![]() | gephyrin | ||||||
![]() | STRUCTURAL PROTEIN / globular alpha/beta fold | ||||||
Function / homology | ![]() : / molybdenum incorporation into molybdenum-molybdopterin complex / Molybdenum cofactor biosynthesis / molybdopterin cofactor biosynthetic process / glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity ...: / molybdenum incorporation into molybdenum-molybdopterin complex / Molybdenum cofactor biosynthesis / molybdopterin cofactor biosynthetic process / glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / postsynaptic specialization / gamma-aminobutyric acid receptor clustering / nitrate reductase activity / Mo-molybdopterin cofactor biosynthetic process / postsynaptic neurotransmitter receptor diffusion trapping / response to metal ion / postsynaptic specialization membrane / molybdopterin cofactor binding / postsynaptic membrane / postsynaptic density / cytoskeleton / dendrite / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schwarz, G. / Schrader, N. / Mendel, R.R. / Hecht, H.-J. / Schindelin, H. | ||||||
![]() | ![]() Title: Crystal structures of human gephyrin and plant Cnx1 G domains: comparative analysis and functional implications. Authors: Schwarz, G. / Schrader, N. / Mendel, R.R. / Hecht, H.J. / Schindelin, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.8 KB | Display | ![]() |
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PDB format | ![]() | 98.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 390.6 KB | Display | ![]() |
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Full document | ![]() | 394.6 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 21.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1eavC ![]() 1di6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | content of the assymetric unit corresponds to the biological active form of the trimeric gephyrin G domain |
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Components
#1: Protein | Mass: 20812.020 Da / Num. of mol.: 3 / Fragment: residues 1-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NA / | #3: Chemical | ChemComp-FMT / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.19 % | ||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: sodium formate, ammonium, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 294K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. all: 71681 / Num. obs: 64743 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.116 / Net I/σ(I): 14.4 | ||||||||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.283 / % possible all: 46.3 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.116 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 46.3 % / Rmerge(I) obs: 0.283 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DI6 Resolution: 1.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: REFMAC library Details: Scaling details: Babinet's principle for scaling has been used. Bulk solvent correction based on constant value has been used. Parameters for mask calculation. VDW prob radii = 1.40, ION ...Details: Scaling details: Babinet's principle for scaling has been used. Bulk solvent correction based on constant value has been used. Parameters for mask calculation. VDW prob radii = 1.40, ION probe radii = 0.80, Shrinkage radii = 0.80
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Solvent computation | Solvent model: bulk solvent correction | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.828 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 4.1 % | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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